Job ID = 6456164 SRX = SRX3270987 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:05:24 prefetch.2.10.7: 1) Downloading 'SRR6159398'... 2020-06-21T11:05:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:42 prefetch.2.10.7: 'SRR6159398' is valid 2020-06-21T11:06:42 prefetch.2.10.7: 1) 'SRR6159398' was downloaded successfully Read 9777089 spots for SRR6159398/SRR6159398.sra Written 9777089 spots for SRR6159398/SRR6159398.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:29 9777089 reads; of these: 9777089 (100.00%) were unpaired; of these: 589324 (6.03%) aligned 0 times 6349427 (64.94%) aligned exactly 1 time 2838338 (29.03%) aligned >1 times 93.97% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1308612 / 9187765 = 0.1424 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 20:11:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:03: 1000000 INFO @ Sun, 21 Jun 2020 20:12:08: 2000000 INFO @ Sun, 21 Jun 2020 20:12:12: 3000000 INFO @ Sun, 21 Jun 2020 20:12:17: 4000000 INFO @ Sun, 21 Jun 2020 20:12:22: 5000000 INFO @ Sun, 21 Jun 2020 20:12:26: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 20:12:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:31: 7000000 INFO @ Sun, 21 Jun 2020 20:12:33: 1000000 INFO @ Sun, 21 Jun 2020 20:12:36: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 20:12:36: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 20:12:36: #1 total tags in treatment: 7879153 INFO @ Sun, 21 Jun 2020 20:12:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:12:36: #1 tags after filtering in treatment: 7879152 INFO @ Sun, 21 Jun 2020 20:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:36: #2 number of paired peaks: 796 WARNING @ Sun, 21 Jun 2020 20:12:36: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:37: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 20:12:37: #2 alternative fragment length(s) may be 4,38 bps INFO @ Sun, 21 Jun 2020 20:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.05_model.r WARNING @ Sun, 21 Jun 2020 20:12:37: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:37: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Sun, 21 Jun 2020 20:12:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:12:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:38: 2000000 INFO @ Sun, 21 Jun 2020 20:12:42: 3000000 INFO @ Sun, 21 Jun 2020 20:12:47: 4000000 INFO @ Sun, 21 Jun 2020 20:12:51: 5000000 INFO @ Sun, 21 Jun 2020 20:12:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:56: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 20:12:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:13:01: 7000000 INFO @ Sun, 21 Jun 2020 20:13:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.05_summits.bed INFO @ Sun, 21 Jun 2020 20:13:01: Done! pass1 - making usageList (513 chroms): 1 millis pass2 - checking and writing primary data (2274 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:13:03: 1000000 INFO @ Sun, 21 Jun 2020 20:13:05: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 20:13:05: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 20:13:05: #1 total tags in treatment: 7879153 INFO @ Sun, 21 Jun 2020 20:13:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:13:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:13:06: #1 tags after filtering in treatment: 7879152 INFO @ Sun, 21 Jun 2020 20:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:13:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:13:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:13:06: #2 number of paired peaks: 796 WARNING @ Sun, 21 Jun 2020 20:13:06: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Sun, 21 Jun 2020 20:13:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:13:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:13:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:13:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:13:06: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 20:13:06: #2 alternative fragment length(s) may be 4,38 bps INFO @ Sun, 21 Jun 2020 20:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.10_model.r WARNING @ Sun, 21 Jun 2020 20:13:06: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:13:06: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Sun, 21 Jun 2020 20:13:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:13:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:13:08: 2000000 INFO @ Sun, 21 Jun 2020 20:13:12: 3000000 INFO @ Sun, 21 Jun 2020 20:13:17: 4000000 INFO @ Sun, 21 Jun 2020 20:13:21: 5000000 INFO @ Sun, 21 Jun 2020 20:13:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:26: 6000000 INFO @ Sun, 21 Jun 2020 20:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.10_summits.bed INFO @ Sun, 21 Jun 2020 20:13:31: Done! INFO @ Sun, 21 Jun 2020 20:13:31: 7000000 pass1 - making usageList (359 chroms): 1 millis pass2 - checking and writing primary data (928 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:13:35: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 20:13:35: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 20:13:35: #1 total tags in treatment: 7879153 INFO @ Sun, 21 Jun 2020 20:13:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:13:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:13:35: #1 tags after filtering in treatment: 7879152 INFO @ Sun, 21 Jun 2020 20:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:13:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:13:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:13:36: #2 number of paired peaks: 796 WARNING @ Sun, 21 Jun 2020 20:13:36: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Sun, 21 Jun 2020 20:13:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:13:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:13:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:13:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:13:36: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 20:13:36: #2 alternative fragment length(s) may be 4,38 bps INFO @ Sun, 21 Jun 2020 20:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.20_model.r WARNING @ Sun, 21 Jun 2020 20:13:36: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:13:36: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Sun, 21 Jun 2020 20:13:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:13:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:13:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:13:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270987/SRX3270987.20_summits.bed INFO @ Sun, 21 Jun 2020 20:14:00: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 5 millis CompletedMACS2peakCalling